The Science of Intrigue
by trenzalore-fields-forever
Summary: AU Clara Oswald has just got the best job she has ever had and a million doors have just opened in front of her. However, when she meets the mysterious Doctor John Smith she becomes fascinated in both him and his reclusive ways. Will she ever find out who he really is and what has made him pull away from life?
1. Hope?

**AU Clara Oswald has just got the best job she has ever had and a million doors have just opened in front of her. However, when she meets the mysterious Doctor John Smith she becomes fascinated in both him and his reclusive ways. Will she ever find out who he really is and what has made him pull away from life?**

**I own nothing unfortunately. I got the idea after watching Charlie St Cloud after the series finale and it implies spoilers but I only see them because I've seen it (and it's so good :D ) also sorry for the bad punctuation, grammar and probably spelling as I am only half awake.**

Torchwood was the leading organisation for scientific research in the UK. The areas they researched spanned from stem cells to space travel and only employed the brilliant and the brightest people in the world. So Clara Oswald applied on chance. Clara was clever but believed herself to be entirely ordinary with a long list of waitress work and shop assistant jobs behind her at only twenty four years of age.

The real reason she applied for a job in the IT department was because her latest placement as a governess had been terminated as the father had met a woman and had become so besotted with her that she had moved in within a few weeks. The woman seemed nice at first when she came round for dinner and always complimented Clara on how beautiful she was and how good she was with the two children. Then she moved in and developed what Clara called 'wicked step-mother syndrome'. The house was rearranged to how she wished it to be, the children had a brand new routine consisting of doing school work for most of the evenings and getting out of the house on weekends so they spent as little time with her and their father as possible, all meals were to be vegetarian and there was to be no meat or fast food consumed in the building. The woman's comments towards Clara turned vile and bitter with the devious look a bully would give their victim. Of course throughout all this the father remained oblivious and saw nothing but perfection in the woman who was far from it in the eyes of everyone else. Then one day Clara snapped. It was at breakfast and everything was fine until the woman 'tripped' and 'spilt' her coffee all over Clara's brand new shirt. All the bottled up feelings came pouring out of her like a waterfall of rage. The woman cried, the father shouted, the children watched in horror as their only source of hope was kicked out of their lives. Clara didn't care about herself, she cared about the children and she had failed them.

Staying with her father until she found a job and a flat, Clara was going for whatever job was going in Central London so the IT vacancy at Torchwood was among many others that went from the bottom of the barrel to the top of the business food chain. For most she had been unsuccessful which had left her in a state of complete hopelessness.

She was lying on her bed in the room she had slept in since she was a little girl. So many dreams had been dreamed in that room and so far non had come true in reality. That was the saddest thing for her; being back with nothing when she left with so much ambition.

Her dad knocked on the door and entered, a phone to his ear and a grin on his face.

" Yes, here she is." He told whoever was on the phone and handed it to Clara giddily.

"Hello?" Clara spoke into the devise nervously and almost jumped at the formal female voice on the other end of the line.

_"Miss Oswald, this is Harriet Jones and I am the executive manager of Torchwood. I am ringing personally to tell you we were all very impressed by your online application and we would very much like you to come down and take up the vacancy. We will give you a six month contract to begin with and if there are no serious issues you will be offered something more permanent. Your job begins next Monday but may I ask you to come in tomorrow to get a tour of the building as you will need to know that as well as the software from top to bottom. I would also like to talk the formalities of you employment. It would really be a pleasure to have you aboard."_

Clara was taken aback by both the job and how enthusiastic this Harriet Jones was about her taking it. Not wanting to give her a reason to rethink her offer however, Clara replied with the same amount of enthusiasm.

"Yes, that would be great. Thank you ever so much I am really grateful for the opportunity."

Harriet Jones continued to tell Clara about what to do upon arriving the next day but she was only half listening. Finally something was happening and in the best way possible. Yet again she would be leaving the house in the morning with all those hopes and dreams she had the first time round.

**Hope you all enjoyed it! let me know if you want it to carry on :)**


	2. First Impressions

**Here's the next chapter thank you all for following and favouriting :D I was going to upload this sooner but I have had some bad news and couldn't finish it last night. Enjoy! **

Torchwood was located in the heart of the jungle of towering skyscrapers that were home to some of the UK's major banks and businesses. At first Clara thought it odd for an organisation focusing on scientific research to be based in the business district in one of the most influential cities in the world. Then, after thinking it over in her head a few times, she concluded that was the safest place for it. A remote base in the countryside with armed guards would be too tempting for those dying to uncover conspiracy at every turn but a huge skyscraper in the middle of the city suggested to the public that what you saw was what you got. Even though nothing is what it seems from the outside, Torchwood had always been shown in a positive light full of success and scientific glory. This made Clara even more excited to begin her new job as she was sure to find out the things nobody else saw and nobody else knew. The secrets of Torchwood would soon be open to her and that made her feel special indeed.

Standing across the street from the magnificent structure, Clara stole a quick moment to take it in for the first time as a future employee. The building was mostly glass yet all you could see in them was the reflection of the sun rays and the blank reflection of the building she was stood under. The building went up strait before abruptly turning into a spike with a steep slant to the west. This made room for what she presumed to be some kind of elegant balcony like in the movies were they had Christmas parties and the occasional do. It was a tall tower yet nowhere near as high as the shard or as dramatic.

Crossing the busy street with a satchel firmly on her shoulder, Clara made her way into the lobby were she promptly froze which resulted in the satchel hitting the marble floor. The walls were mirrors yet tinted an electric blue that made everyone's reflections look like aliens. The lifts to the endless count of floors were arranged in a circle and went up through the centre of the building, surrounded by giant decorative models of DNA molecules, atoms and glass dinosaur skeletons. The lobby area was busy with men in suits talking about the possibility of beating the speed of light and women in lab coats arguing over whether cloning was ethically right or not. It reminded Clara of the time her parents took her to a seminar on plant growth when she was failing GCSE science. She learnt nothing but it was a good day out. The only reason she remembered it was because it was one of the last family days out with her mother.

Once the amazement had washed away, Clara felt rather lost. There were many desks and many people yet she did not know which ones would take her were she needed to go. After wandering around for half an hour, Clara noticed a professional looking woman heading over from the lifts. She greeted Clara with a handshake and pinned a name badge to her maroon coloured t-shirt.

"Miss Oswald, I am Yvonne Hartman and I will be taking you on the tour of this magnificent building". The woman introduced herself with a smile Clara had seen on that evil stepmother. A false smile. From what Clara had deduced from her in the first few moments, Yvonne appeared to be living in her own self importance. If the confident strut across the lobby wasn't a big give away then the casual flick of her perfect blonde hair was as good as a written confession.

Knowing that this Yvonne woman had the power to dismiss her on the spot, Clara fake smiled back. "Great, may I ask how you knew it was me? I mean to my knowledge I did not give a picture with my application".

Yvonne smiled at her as if she were an innocent child in a rather demeaning way. "Do you really think we would hire someone according to their application alone? We web-searched you to make sure you were up to the mark. As you can tell you are. Nice holiday pictures by the way."

Clara's mouth hung open as Yvonne began to walk away. Luckily for her she had more online dignity than most of her friends otherwise she wouldn't have even made it to the short list. Hurrying to catch Yvonne up and huddling into a crowded lift with her, Clara's heart had filled with butterflies as the lift began to move towards her first stop on the magical mystery tour.

**I had to end it with a Beatles quote as it was just too tempting :) Hope you all liked it and I'm sorry it doesn't get very far and doesn't make much sense. The next chapter will be much better I promise :)**


	3. Magical Mystery Tour Part 1

**Thank you all for following and I'm sorry I haven't uploaded anything for the past few days so I decided to give you the part of the next chapter I have done so far and I will hopefully give upload the rest tomorrow. I think this is the worst bit so far but it is kind of an establishing chapter to get the story really started so be kind :/ Remember I am not the most literate person in the world. Hope you all enjoy!**

The lift door closed, trapping them in the small space and blocking them from the loud chatter in the reception. Clara waited for the lift to do make her stomach sink as it began to move but it never came. She waited a few seconds before she started panicking. Claustrophobia was not something Clara really suffered from but in that small still lift with all those people, she felt her heart rate increase.

"The lifts stuck" she cried, trying to push her way towards the panel of buttons before Yvonne pulled her back.

"The lift is designed so you don't feel it move. That way those working at the very top don't get motion sickness. This lift system is the fastest in the world so it is kind of like a high speed drop ride at a theme park . We are almost higher than the tip of Big Ben now."

Clara relaxed and apologized to the others in the lift who waved it off as first day naivety. The lift opened moments later and Yvonne escorted her out onto the floor titled 'archaeological science'.

"Why did we skip all those floors?" Clara asked as they walked down a corridor with walls of white tinted glass.

Yvonne's heels echoed against the white, hard, cold-looking floor like a female villain in a film which made Clara like her even less. When she was a child she feared a woman like her and the grown up Clara had made a mental note to keep an eye out for any Dalmatians.

"They are admin. Your job will be based on the actual departments."The older woman informed her."The original place you applied for was for admin but you were just too good an applicant for you to spend your days changing the page layout on a document. The software up here is so advanced that some are capable to produce three-dimensional images that can be moved and changed by hand movements. Quite impressive, isn't it?"

Clara shrugged "I saw that in Iron Man".

Yvonne frowned and began to brag yet again. "This department is the best of it's kind in the British Empire..."

"There is no British Empire" Clara pointed out. "I wasn't great at history but I do know what the Common Wealth is".

"We'll see" Yvonne replied before continuing with what appeared like a sale pitch. "Here, we are making advances in archaeological science that could change archaeological deductions from being estimations to cold hard fact. I can't take all the glory though as Professor Pond has worked very hard making all these great discoveries."

They reached a door that was made of glass similar to what had surrounded Clara for the past two minutes but this time she could see a figure moving on the other side. Yvonne pulled a card from her pocket and swiped it on a panel attached to the wall. There was a high-pitched beep and the door slid open.

"The doors are all electronic so the building can be on lock down if infiltrated and in case there is contamination in the Medical department that could threaten the public. You will be given this upon taking the job."

Clara still wasn't impressed as she was either going to be protected or imprisoned by doors similar to those at her local supermarket. However, once the door opened to reveal the lab hidden behind it, she could no longer try and defy Yvonne's annoying bragging. The lab's floor pan was gigantic and even then there were still doors that men and women in scrubs were popping in and out of with test tubes and see through sample bags. The walls were covered in screens that showed facial reconstructions, Computer generated images of decaying bone marrow and live feeds of what appeared to be autopsies on ancient skeletons. All the equipment was all shinning as though it had all been brought in moments ago. It was like Star Trek meet Silent Witness.

A door opened close to them and a red haired woman in a lab coat appeared. At first, Clara thought she must have been an intern as she looked to be a similar age as herself but as soon as Yvonne greeted her with 'Professor', she was both surprised and impressed.

"Clara, this Professor Amelia Pond, the head of this department. Amelia, this is Clara, the new technician I informed you about". Yvonne introduced them and the pair shook hands.

After a quick run down of the software used in the department, Yvonne excused herself to make a phone call. This was music to Clara's ears.

"She is really getting on my nerves" Clara huffed, making Professor Pond laugh.

"She calls me Amelia and I hate that" the Professor replied in a Scottish accent. "Amelia's my real name but I prefer Amy".

"I will remember not to make the same mistake" Clara promised. "How did you become so interested in all this?"

Amy stole a glance to were Yvonne stood before she whispered her reply.

"I was really studying Classic History when the head of department before me came in for a talk on Roman life. I was so inspired that I stayed at the end to ask more questions. Soon I became like an apprentice to her and she pulled some strings to get me a job here. Don't tell Yvonne as I am meant to be here to develop archaeological science, not to make my own discoveries. No one else minds but she is like vermin. She never used to bother with this department before I became the boss and now she is here at least twice a day."

"I bet the old boss must have put Yvonne in her place at some point" Clara laughed and Amy nodded.

"She did all the time. I wish she could be here now, I think everyone does to be honest."

Amy's voice was sad so Clara decided not to pry anymore. The last thing she wanted was to upset her as Amy seemed like someone she could easily get along with. Yvonne returned and told Clara they were behind so had to skip some of the departments and gave her enough time to say goodbye to Amy before escorting her back towards the lifts.

**I made Amy a archaeological scientist as she said that her favourite topic when she was a kid was the Romans in 'The Pandorica Opens' and it links with what is going to happen later on. Sorry to those who know the science as I really don't (I'm a D) and sorry for a bad chapter :/ I will try upload more tomorrow and since I have a week off I will be writing a lot to put off revision. **

**Also if anyone has seen Broadchurch and ships Alec and Ellie, would you read a weird fic I have been plotting about them both during the case? Let me know if you would and I will upload it :)**


	4. Magical Mystery Tour Part 2

**Here is the second part! Thank you for guys following and thank you for the great reviews. The next chapter will be up in the next two days :) enjoy :)**

The next floor they arrived at was titled 'Medical Science'. The glass was tinted red this time which Clara found very unpleasant.

"Why is the glass a different colour" she asked Yvonne who was strutting ahead like before.

"Each department is colour coded. This is coded red. Very fitting don't you think?" Yvonne replied before swiping the door yet again.

Unlike the lab in Archaeological Science, this one was mostly test tubes and computers with diagrams of organs plastered onto the walls. All the people were in lab coats, not scrubs and this time they were not greeted by a red headed woman but a man with short, light brown hair.

"Hello" he said before shaking Clara's hand awkwardly. "I am Doctor Williams, call me Rory. My Wife sent me a text a few seconds go telling me you were coming, Clara."

"Your wife?" Clara questioned and before she caught on. "Oh Amy's your wife."

Rory nodded proudly and smiled at the mention of Amy's name. "Yes, we got married in 2010".

"She's a lovely woman your wife. So what do you actually do around here?" Clara asked Rory but Yvonne decided to cut in.

"This department focuses on developments in how to cure illnesses, how to make the survival rate of major surgery higher and much more. Some day we will be able to cure everything and that will be because of this department."

"Well, not really" Rory corrected her. "As we evolve, so do the illnesses. We are in a constant battle with nature but what I personally aim to sustain is a way to keep on top of it all. I mean once one disease is curable then we must move on to the next one. There will always be a next one as that is the way it goes."

"Thank you, Doctor Williams." Yvonne snapped, embarrassed after being proven wrong. "We do a lot of work in this department. There used to be a number of different departments specializing in different areas of medical science but we had budget cuts. This is a recession after all."

Rory looked at Yvonne as though she had said something untoward. Clara looked between the pair but before she had chance to ask another question, Yvonne told her they needed to visit another departments and Harriet Jones was expecting them in an hour.

"Nice to meet you, Rory." Clara called over her shoulder as she followed Yvonne out of the lab.

Rory waved and replied "You too Clara. Don't be a stranger."

"Why did we skip two floors?" Clara asked as they walked out of the lift onto a floor tinted blue. Yvonne had shown her Biomedical Engineering, Pharmacology, Physiology, Astrophysics, and Zoology and by now Clara was ready to go home. The first two had been interesting as Amy and Rory were interesting people. The head of the other departments were all in their mid 50's to early 60's and were as dull as a brick. So far they had gone up floor by floor and were now at the very top. The floor she skipped did not have silver buttons like the others, but red ones. This intrigued Clara and she began wondering what conspiracies lay at the touch of those buttons.

"They are off limits. If you are needed there, you will be briefed when the time comes. Company policy." Yvonne told her before she stopped and turned to face her. "If you go onto those floors without permission, you will be out of here so fast that your feet won't touch the ground. You understand?"

Clara nodded nervously. As well as being annoying and up herself, Yvonne was a scary woman.

There was no label to this floor which surprised Clara. Also Yvonne had said nothing about what was behind the blue door. When the door opened, Clara saw why there was no name for this floor and why Yvonne could not explain what the floor consisted of. This was not a lab, this was a huge workshop with only one occupant. A goofy looking man in a bow tie.

The man was sat a few metres away at a desk covered in paperwork and spare parts from machines with a single photo frame near a standard office computer. He was looking at the frame with sadness in his eyes and appeared to be completely oblivious to their presence.

Yvonne cleared her throat and he looked up. He moved a stand of his brown, floppy hair away from his right eye and got up to meet them.

"Yvonne, what can I do for you?" He asked before looking Clara up and down. "Whose this?"

"Doctor, this is Clara Oswald. She is the technician I told you about this morning." Yvonne told the man and he instantly took hold of Clara's hand and shook it.

"Oh, hello. I am the Doctor. Just the Doctor. I stay up here and make things. It started as a hobby but I ended up becoming quite good at it. I have various projects running at the moment but they all need little adjustments."

Just as he said that there was a huge bang and sparks flew into the air from the far corner of the workshop.

The Doctor bit his knuckles before turning back to Clara. "I will fix that later. So, Clara Oswald. Do you have any hobbies?"

"I makesouffles" she replied, feeling rather boring compared to this man but he appeared to be fascinated by this.

"Really? Could you make me one? How could you make the perfect souffle I wonder? Maybe I could make a machine. The world needs more souffles." He was rambling and Yvonne didn't like it.

"Doctor" she warned him and he mouthed 'sorry' at her before looking at Clara again.

"My computer system is faulty most of the time because I sometimes tinker with it but the software isn't advanced enough for my changes so it just all crashes. Sometimes it works but I would like you to double check that too. Do you want to see the new telescope I am working on. Through it, you can see the surface of mars down to the last rock. Soon, I will be able to see past Pluto if all the planets stay out of the way. Amazing, isn't it."

"Very much so" Clara replied. "Maybe next time. I have a meeting to attend. Wouldn't want to upset the boss before I even get started."

"That's right" Yvonne agreed. "We better get going now. I will be back later for those reports Doctor. I want them done and I want them done by then. Is that clear?"

"Crystal" he replied. "See you then. Goodbye Souffle Girl."

Harriet Jones was just how Clara imagined her to be. A small woman who was married to the job. Miss Jones's office had one personal picture off an elderly woman and the rest were all to do with the company. On the walls there were awards she and the company had learnt over the years. One thing caught Clara's eye however. It was the only painting in the room and it was of an old man in Victorian upper class attire. The painting looked old and worn and felt out of place in a modern building such as this one.

"Impressive, isn't it." Miss Jones said once she followed Clara's gaze. " That is Kazran Sardick. He founded the company over a hundred years ago."

Clara looked at the picture for a few more moments before turning her attention to Miss Jones. Unlike Yvonne, Amy and Rory, she could not call this woman by her first name. She was way too professional.

"Clara Oswald, this is not an interview" Miss Jones told her. "This is a meeting to discuss your employment if you are to take the job. I must ask you now, before anything else, that you will not speak to anyone who is not under the companies employment about what you will see in this building. Is that clear?"

"Crystal" Clara replied, causing Miss Jones to smile.

"Good. Now I must inform you of the rules you will be obligated to follow during your employment here. You must not go to the floors that are labeled with red buttons in the lifts without being instructed to do so, you must never go down to the vaults as they are completely out of bounds, you must keep out of any drama or conspiracies that develop in the departments, and you must ignore any contact made from our rival companies. When you break a rule, you receive a strike. Three strikes and you are gone, is that clear?"

Clara nodded.

Miss Jones smiled again and placed a pen and a piece of paper in front of Clara.

"All you have to do is sign there and you will be one of us."

Picking up the pen, Clara hovered it over the dotted line. All it would take was one signature and she would have the best job she could ever hope for. Her life would change with a squiggle of ink. Signing her name quickly, Clara handed the paper back to Miss Jones who filled it away in a draw.

"Welcome aboard, Clara Oswald."

**Hope you guys liked that. The next chapter will be when the story really kicks off. ;)**


	5. Talking and Jammy Dodgers

**Sorry about how late this chapter is as I've had a busy few days. Thank you all for following and reviewing and I hope you enjoy!**

****For the first time in Clara's professional life, she had her own little office. It was small and barely had enough room for the desk, the filling cabinet and the two leather swivel chairs that were ready and waiting for her on her first day. She had been escorted to a floor in the middle of the admin floors that consisted mostly of offices. Not the executive ones though as they were on the second floor. These offices were simple, small and designed so their occupants spent as little time in them as possible. Some had desktop computers but Clara, being a technician to the highly advanced labs, was given a slim silver laptop that was apparently made especially for her. Whoever decided on treating her had made Clara feel much more relaxed.

Upon leaving after signing her contract, Clara was given a pack with information about the overall software of the building. The whole building was run on the same computer system that controlled everything from the doors in the lobby to the programs used to digitally reconstruct organs, reactions and the faces of Amy's Romans. This was filed under the name 'T.G.I' and at first glance Clara thought it said CGI but realized these initials were completely unknown to her. She found the theory of the computer system to be relatively easy to learn and the firewalls rather simple. After reading threw her pack a few times, she concluded that she had only been given the information she needed and there was more to this T.G.I. than meets the eye.

Clara's office also came with a red telephone and when it rang a silence smashing ring for the first time, she jumped out of her chair so quickly that it hurt her left knee.

"Hello?" she answered it nervously and was revealed when the voice was a familiar and friendly one.

"Hello, it's The Doctor here" he practically shouted down the phone. "I was wondering if you could come and have a look at my computer as it has gone all wibbly wobbly."

"Yes, of course." she replied. "I'll be there in no time."

He thanked her and hung up. Clara couldn't be more thankful that he was her first call out. The last thing she wanted was to start off with one of the more serious scientists or Yvonne.

The Doctor was waiting for her and greeted her as though she was an old friend that he hadn't seen in months and not someone he had met once in a fleeting visit less than a week ago.

"Souffle girl" he grinned as he led her over to the computer. "The screen went blank and it all switched off. I don't know what happened." He frowned at the object, causing her to giggle.

"Sir.." she began but he gasped as though she had offended him greatly.

"Doctor, that is what everyone calls me. Sir makes me sound boring." He spoke like an upset child which made Clara giggle even more.

"_Doctor_ is anything working?" She asked and The Doctor shook his head. Rolling her eyes, Clara left the computer and headed across to the door. "I learnt while revising how this place works. The computer controls the electricity so nothing is ever really turned off as it is a permanently running system. However, if it was always kept on in each department 24/7 then the electric bill on this place would be colossal compared to what they are actually being charged for. They keep the costs down by putting a power down leaver on each floor which will turn it off completely. Lights don't count due to health and safety so it's easy not to notice. I wouldn't if I hadn't gone over it repetitively since I last came here."

Clara found the lever and pulled it up. Suddenly the room was filled with flashing lights and beeps of every pitch possible. The computer screen lite up and The Doctor clapped. "Well done."

She walked back over to where he stood and glared at him. "You knew that was the problem as who else would switch it off."

The Doctor shifted a little before nodding. "Sorry, I wanted you to come talk to me. Rory is doing a lecture at some university and Amy has been given a new project so I thought of you."

Clara sighed and sat herself down in his swivel chair that was identical to hers but was more warn and even burnt in places. "Fine, I'll stay but if Yvonne catches me..."

"I will take the blame and everything will be fine" he assured her. "Yvonne can't sack anyone anyway. That power is down to the boss and the boss only. Yvonne likes to pretend and it's easier to just go along with it than argue. Even the heads of the departments can't sack their assistants and can't even give anyone a written warning. That's been the way since the company began."

"Do you know a lot about the company?" Clara asked him and he nodded, perching himself in front of her on the edge of the desk.

"I know a fair bit. More than most but of course there are a lot more things I don't know." He replied, finding a pack of Jammy Dodgers under all the mess on his desk and offering her one.

Clara took it gratefully as she had skipped breakfast that morning as she was determined not to be late. "Thank you. So do you know what T.G.I. stands for?" she asked before taking the first bite into the biscuit.

"Telegraphic generated interface. That's what Yvonne told me anyway." He spoke with half a Jammy Dodger in his mouth but thanks to her time looking after two children, Clara had mastered the art of understanding someone with their mouth full.

"So is it really as simple as it looks? I mean I have had computers with more firewalls than this has" she told him and chuckled.

"Clara, nothing is ever as simple as it looks" The Doctor said wisely."You are more complicated then you look and so am I. We try and hide the complicated stuff for loads of different reasons, mostly to protect ourselves and others. We don't know half the stuff that goes on round here for our own protection."

Clara looked at him in surprise "so you accept that?"

"Of course not" he replied with a cheeky grin."I am dying to get into those vaults and see what they are hiding down there."

"Well what would you do with the information?"

"Nothing" he replied. "I just want the adventure."

For a moment, Clara had questioned her judgement on The Doctor but now she knew she was right about him. He lived for the thrill.

**Clue for next time..."Whose River Song?"**


	6. Whose River Song?

**Next Chapter woop woop. Thanks for Following and Favouriting! Sorry it has taken so long to upload this but I have been revising most of the week. Enjoy!**

After two weeks of being called unnecessarily by The Doctor so he could 'show her his new bow tie' and 'introduce her to his favourite biscuit of the day', Clara decided that he had the personality of a child and the intelligence of someone who had lived a thousand years. Amy and Rory were just as bad but they didn't interrupt her working day. They seemed to have the same lunch break as Clara and insisted on going wherever she went. Sometimes The Doctor came along too but he was usually to busy breaking something and eating biscuits to bother with a proper meal.

It was a Friday and Clara was trying to help The Doctor program the new devise he was working on. 'The Face Matcher' was his latest project that he had begun months before Clara met him and it's job was to search the internet and the Torchwood archives when a face was scanned in. The Doctor told her that the machine would be able to tell the difference between the most identical twins and match a picture of an eighty year old to their sixteen year old self. Even though she thought it was impossible, Clara helped him as she could see the happiness in his eyes when he worked on the impossible idea and didn't have the heart to put him straight. Then again she was nowhere near as clever as The Doctor so he may have in fact found a way to do it. However, until she was given evidence, Clara did not side with it being either fantasy or reality.

"Amy and Rory have invited me to out with them tonight" Clara told him as she watched him tinker with a busy, colourful circuit of wires. The Doctor didn't look up or show any interest in what she said so she came out and said what she was implying. "Do you want to come too?"

"No" he said instantly and lifted his head. The childlike expression Clara was so used to had disappeared and was replaced by the expression of an old man. A lonely old man. "I like to stay here late or go straight home."

"Oh?" Clara was surprised by this as she saw The Doctor as a man in love with life. "Why is that?" She asked.

"I just like having time to myself" he replied and then continued with his work.

Amy and Rory took Clara to a small pub close to were they lived. The pub was small and quiet which allowed the trio to get a good table in the corner closest to the bar.

"I asked The Doctor to come" Clara told them which caused Rory to gulp down his drink quickly.

"What did he say?" Amy asked, a look on concern on her face. "He didn't shout at you did he?"

Clara shook her head. "Why would he?"

Rory looked at Amy who nodded and he got up, excusing himself to go sit at the bar.

Amy sighed and put a hand to her forehead. "I don't know what to say" she admitted.

"Just tell me why" Clara told her, eager to know why the pair were acting strangely.

"The Doctor is a brilliant man as you know" Amy began. "He is not like you or I but has feelings all the same. The problem is when a brilliant man has feelings, the affects are different form when we do. Love is strong and grief is unbearable. That is the reason why The Doctor is how he is. Love and grief."

"But he is so happy all the time" Clara argued. "How can a grieving man be so happy."

"Because he doesn't want anyone to know how much pain he's in. He's The Doctor, the brain of the company. He doesn't want to look how he feels. Me and Rory can tell as before he used to be different. He always said River Song was the best part of him and it looked like he was right."

"Whose River Song?" Clara asked which caused Amy to bite her lip.

"She was the one who got me the job. The old head of my department who gave the talk about Romans. She was here before me and before Rory. She was there when the old Doctor was there."

"Old Doctor?"

"The title comes with the job" she explained. "The Doctor you know started just before me. The reason why they use the title is because their intelligence could put them in harms way. River was the only one to know our Doctors name."

"Was?" Clara gasped "you mean she's.."

"Dead, yes" Amy replied gravely. "She died less the six months ago."

Clara gave her condolences to which Amy assured her she was fine. This gave Clara the drive to ask more.

"So why is The Doctor so upset may I ask?"

Amy was silent for a while before looking down at the wooden table. "She was his wife."

Clara was on complete shock. The Doctor, the happy man who shared jammy dodgers, had been widowed less than half a year ago. How could he put on such an act?

Against her better judgement, Clara asked one more question. Just one.

"How did she die?"

**I will upload the next chapter hopefully next weekend as I have exams all this week. Sorry for all the waiting but I will make up for it as soon as I finish :)**


	7. Amy's View

**Here it is! Sorry for the wait but I have a 10 week holiday now so hopefully I will be able to update with only a few days wait. Enjoy!**

_177 days earlier._

Amelia Pond woke up early that morning with a banging headache. Rory was still fast asleep, tired after a hard days work. However, Amy was not tired as her dear friend River had allowed her to go home early which gave her the opportunity to catch forty winks.

After a long time trying and failing to regain a dreaming state, Amy got up slowly so she would not wake her husband and crept downstairs to make a coffee. Nothing was on the TV except for repeats so she turned on her computer to check her emails and do some work.

In the five hours since she last checked her inbox, Amy had two new emails. One was yet another request for her to take a job at Columbia University teaching archaeology. They had contacted her at least eleven times and each time she had refused point blank due to the fact that she couldn't leave Rory. However, this time they had made an interesting offer. There was now a place in the medical centre and the place could be Rory's if she accepted. That changed things. Amy had always wanted to live in America for a few years at least but Rory would see it is a God send. Since he became interested in the medical profession, Rory had always dreamed of being 'more than just a nurse'. He was already but this was a chance for him to inspire others and to find a tiny bit of normality. The work load would be less and so would the hours which would mean more free time for them. Then there was the position she had been offered, one were she could look at the actual art of archaeology instead of the art of bone decay day in and day out.

The other email, however, snapped her out of the american dream. The message was from River and it read _Yvonne has told me the department will live another day. They are going to cut some of the admin instead which means we must be doing well. I cannot thank you enough for all your work over the time you have worked for me. In fact, besides my husband, you are the best thing that has happened to me over the past few years. See you at work and don't you dare be late. All my love, River. P.S. we were wondering if you and Rory wanted to escape to the country at one point. Maybe in the summer months?_

Now there was no way she could accept the job. Could she really let her closest friends down? But then could she live with the thought of preventing her husband's dream? Either way she was going to regret her decision when it came down to it.

The Ponds arrived in to work via the tube as they did every morning and were met in the lobby by The Doctor and River Song.

"Hello Ponds" The Doctor greeted them in his usual manner. River simply rolled her eyes at him and said good morning to the pair.

"It's good to hear about the department. You have done a great job" Amy congratulated River who slapped her playfully on the arm.

"We both did a great job" she corrected her young friend. "When I do leave, I will be happy to know such a great person was taking over."

Amy blushed, a little overwhelmed by all the flattery she had been receiving recently.

"So you are positive the department will stay open?" Rory asked and River shrugged in reply.

"It will as long as I'm alive. After that I do not know. All I can say is as long as there is a breath in my body, I will not let that foul woman take away my livelihood."

"You would still have me though" The Doctor pointed out. "All though I would rather not be cut up like your clients."

River looked at him with the all but familiar flirtatious look in her eye. "You would never be a client, sweetie."

At this, The Doctor turned a bright shade of red which made the others giggle and tease him. This was an ordinary morning like any other. Little did they know it would be the last.

Amy was in the middle of a report when River entered the office they both shared. To her surprise, River was stressing, panicking even.

"Have you seen the blue diary on my desk?" she asked and Amy shook her head. River's diary was battered and filled with, what Amy could only guess, wonderful ideas and theories. The book was the bluest blue and resembled the outside of a 1930's Police Box. The only reason Amy knew they existed was due to River's love for them. During those first few weeks at Torchwood, River would calm her down from the chaos of the scientific world by telling her stories of hiding in the decommissioned blue police box near her house and pretending it was a magical machine that took her on adventures.

River began to search through the scattered documents that littered her large desk, breathing frantically and shaking uncontrollably.

"River, what's the matter?" Amy asked but she never got the answer. River simply stopped what she was doing and smiled at her.

"Nothing Amy. Nothing is the matter" she assured her before dashing out of the room. Amy always knew River was no ordinary woman but she was acting very out of character.

It was almost two o'clock when River returned, linking arms with The Doctor. If Amy was not equally happily married, the sight would have made her jealous of the love they clearly had for each other. The Doctor cared about River and would pull out all the stops to help her or make her smile. In turn, River would give The Doctor something he had never had, a constant. The Doctor told Amy long ago when River was away on a university tour in America that the life of a genius was a lonely one and River was the only thing he could trust to always be there. That taught Amy a valuable lesson which she was sure also related to her and Rory. Everyone needed someone.

"Has the diary turned up yet, Pond?" The Doctor asked, leaving River to sit on his best friends desk.

Amy had searched the office top to bottom and still there was no diary. She had checked the whole lab twice yet the blue book remained lost. River assured her that it would turn up and commented that 'it was near enough full anyway'.

"Shall I make a diary finding device?" The Doctor suggested but River shook her head.

"Sweetie, don't worry about it. All I want to do is go have a drink."

"Me and Rory are free if you want to come round" Amy offered. "I bought some of that nice wine from that posh shop on the high street the other day."

River agreed instantly but The Doctor frowned like a sulking child. "I hate wine" he grumbled. "It tastes all weird and blah."

Amy laughed and threw a pen at him. "No one said you had to drink it. Anyway, Rory won't be drinking as he is doing a transplant surgery at the hospital tomorrow and he needs a clear and focused mind."

"So why can you two drink?" The Doctor asked in confusion. "You do operations every day."

"Yes, sweetie, but the people we are operating on have not been able to complain for hundreds of years. Also we hardly ever do the dirty work. We just examine what we are given" River explained to him.

The Doctor jumped off Amy's desk and kissed River's hand. "I will come pick you up on my way down. Keep that Pond out of trouble." He pulled a face at Amy and took one last look at his wife before leaving.

Everything had been cleared up and the rest of the department had gone home. Amy sat at her desk, waiting for River to return so she could lock up. Her friend had been gone a while even though she was only going to get a coffee but this was far from unusual as Yvonne hovered around the coffee machine like a vulture over a battlefield. The pair were probably screaming at each other at that moment. She believed this for a while. Until The Doctor scampered through the lab and into the office, tears streaming his face and a frantic look in his eyes.

"R-River..."he sobbed, dragging Amy from her seat and out of the office. "I Ju-Just found her there when I had finished up and I do-I don't know what to do."

He pulled Amy into the lift and pressed the button that took them to his workshop. The doors of the lift opened and then everything went slow for Amy. The Doctor's sobbing and cries were mere mumbles in the background of the loud, throbbing silence that had surrounded her like a bubble. Each breath became harder and each heartbeat banged harder against her rib cage.

River lay in the corridor on her right side, her body curled in a ball with her hands resting by her face. Her blonde hair was stained by the pool of blood that surrounded the upper part of her body. River Song was dead and had died mere metres away from were her husband had sat making her a new diary.

**Bit depressing but here we are. The next chapter will be back with Clara but I wanted to do this chapter to set the main story line Hope you all liked it and I will hopefully update this within a few days :)**


	8. Could It Be?

**Sorry for this chapter being late but I have had a few distractions. Enjoy!**

Clara had spent her weekend reading. She could tell him that without lying and without telling him the truth. She had been reading but the book was rather intrusive to her friends life. _Discovering Rome's Secrets_ by River Song. After returning home after that night out with the Ponds, Clara did a little digging on the mystery which was River Song. All she found was professional stuff which disappointed her somewhat but when she saw River Song had a book, Clara thought of one thing. About the Author.

The book itself was rather interesting and actually made Clara enjoy history, a subject she had never really liked. There was no description about Professor Song but one thing caught Clara's eye. The book began with a thank you. This caught her eye as after telling the gruesome tale, Amy had gone on to inform Clara that the police ruled the cause of death as being suicide as 'there was no sign of a struggle, no attempt to get away, and no evidence of there being anyone else of the top floor.' They had accused The Doctor but that was soon dropped after no solid evidence could be given. They concluded that River was 'unhappy in her marriage' and 'wanted a way out'. However, the thank you suggested otherwise.

_I would like to say thank you to my loving husband who without his enthusiasm and love, I would not be the person I am today. My love fro you is eternal and I cannot be more lucky to have you look upon me with your beautiful eyes._

_"Never, never, before Heaven, have I thought of you but as the single, bright, pure, blessed recollection of my boyhood and my youth. Never have I from the first, and never shall I to the last, regard your part in my life, but as something sacred, never to be lightly thought of, never to be esteemed enough, never, until death, to be forgotten."_

In Clara's personal opinion, these were not the words of an unhappy woman. The book had been published two months before she died and Amy had told her the book was a quick 'slap-bang' job. These words were the words of a woman in love, not a woman in misery.

Clara discussed this with Amy on Monday morning in her office but received a rather negative reaction.

"Clara, you can never know what goes on in a persons head" Amy told her sternly. "It may have been a spare of the moment thing, she may have planned it or she may have been murdered. We will never know and I don't really want to know. I think to keep the end open and not closed as that would mean accepting the truth. Also I would rather you not stare up all this mess again as The Doctor has barely got over the shock of what happened. You could send him over the edge and I can't lose anyone else."

"But the thank you.." Clara began to argue but Amy cut her off.

"She said a few sentences and quoted Dickens. Anyone could do that. She may have been happy with him but not about other things. At the end of the day she's dead. Not amount of searching for answers can bring her back."

Clara could see Amy's distress and anyone with less courage than herself would have let her be. However, Clara Oswald was as brave as a lioness when it came to standing up for what she believed in and was a good negotiator.

"You search for the facts behind an ancient bodies demise yet you are uninterested in your friends. I am not asking for you to assist me but to help me with one small detail. The diary, were is it?"

Amy was still for a few moments before shrugging. "The diary was never found."

"So if someone had it then they would have some knowledge of what happened, correct?"

"Oh my God, I guess they should have a notion" Amy gasped. "How did this not come up before?"

"I have no idea" Clara replied. "Also, what was the actual cause of death?"

Amy though for a second and began to pace up and down the small room. "They said she was hit by something over the head but it was something else that killed her. The police said she must have taken something and then hit her head. But when I think about it, there were no bloody patches in the lifts or on the walls."

Clara looked at her feet, deep in thought. "Don't tell The Doctor I know."

Amy laughed and shook her head. "Do you really think I would tell The Doctor that I was gossiping about him. He would let one of his mad robots lose on me and that would cause more harm than he wants it to."

Giving her friend a small smile, Clara turned away from her. What was going on here? Why would the police come up with such a faulty story? Why was the death of an archaeologist a huge conspiracy?

She was adamant to find out the truth behind the death of River Song.

**There you go. It's bad but at least now you know what the story arc will be :) The next chapter will be a little adventure between The Doctor and Clara. The quote is from ****_Dombey and Son_**** by Charles Dickens.**


	9. The One With Braveheart Clara

**Double whammy! Thought as I broke my promise of updating within a few days that I would give you another chapter. This is kind of a short story based on the Crimson Horror episode so it may (I doubt it but possibly) have some spoilers. Also I apologies for this Friends style title but it's in my head as I have been watching it a lot this week (I'd say too much but, like Doctor Who, you can never have enough of Friends). Enjoy!**

Clara and The Doctor were eating lunch in the small canteen on the fifth floor, sitting alone on a table far away from were the other groups of gossiping secretaries and debating scientists. Amy and Rory had taken the day off for a family wedding which left the remaining pair at a loss of what to do. Especially since The Doctor had caused an explosion in his workshop which meant it was out of bounds until the repairs were made. Yvonne had given him a spare office and a large pile of paperwork. So naturally, The Doctor decided to follow Clara around. Clara was finishing her lunch while The Doctor read about the latest disappearance in the paper. Men and women in their twenties had been disappearing in the area surrounding the business sector which had caused some arguments in the Oswald household. Apparently dads never lose their protective tendencies towards their daughters.

"I am going to have to go do some work soon" Clara told him as she put some milk into her tea.

"No" The Doctor protested like a child not wanting to go to school. "Please don't leave me. I can't sit and do paperwork all day! It's so boring!"

"An hour or so won't hurt" she told him with a giggle. She loved seeing his childish side, especially as she knew the real horrors that haunted him.

At that moment, an old woman wondered into the canteen. She had a face that reminded Clara of the old lady that used to live in a raggedy bungalow down her street who used to come out and threaten the children with her walking stick if they walked on her lawn or loitered outside her house. The woman had a specific distaste to the eight year-old Clara and would come out whenever she saw the girl playing in the street without a parent present. That memory alone made Clara's first impression of this old woman as a negative one as much as she resented herself for it.

"Who is that?" she asked The Doctor who followed her gaze and frowned.

"That's Winifred Gillyflower but everyone calls her Mrs Gillyflower" he huffed, glaring at the woman. "She's a _prize-winning chemist and mechanical engineer_" he mocked her spitefully which surprised Clara. The Doctor didn't seem like the person to hold grudges.

"What's she done to upset you?" Clara asked in amusement.

"She shamed me in front of everyone just because I put a gear in the wrong place" he growled. "Also she stole a Jammy Dodger from my plate at the Christmas party. There are some things that are morally wrong, Clara."

Rolling her eyes, Clara watched Mrs Gillyflower get two sandwiches, two teas and two slices of cake from the counter before leaving swiftly.

"Does she do that every day?" Clara asked and The Doctor nodded.

"Yes, she is greedy and eats everything, even if it is someone else's Jammy Dodger."

"Does she work with anyone?" she asked and yet again he answered with a scowl.

"No she doesn't. She likes to have all the credit and always brags that _she's an old lady yet she can do better than everyone else on her own._ Well lets see her try make a machine that matches faces exactly."

"Doctor focus" Clara snapped, hitting him with his newspaper. "Two sandwiches and two cakes are fine but two teas too? that's a little weird don't you think?"

The Doctor shook his head and snatched back his paper. "She's lazy and can't be bothered to come back for another."

As he was in a fowl mood, Clara took her tea back to her office and kept away from him for the rest of the day.

Clara woke up to find her computer on sleep mode, her phone out of charge and the sky dark outside. The clock on the wall said ten to six yet she remembered it last being half three. She had been asleep a while. Sighing, she stood up to quickly and went dizzy. Now well and truly ready to end the day, Clara got her things and headed towards the lift. All the other offices were dark and empty which meant she was responsible for turning off the power which she always hated as it meant standing in the dark for a few moments before the lift came. In that darkness she could here the creaking of the building as it stood it's ground against the wind, the humming of the machines above that were still active and occasionally the muffled voices of the people above. In darkness, sound becomes haunting. However, this time she heard footsteps in the darkness, coming closer and closer. Sh reached for a phone to shed some light on the situation but she remembered it was dead. She stood still, hoping the lift would come soon and that whoever it was, may it be friend or foe, would not see her before hand. However, she soon felt a breath on the back of her neck and the smell of mint and a harsh chemical permeated the air. Before she could scream, a female hand clamped over her mouth and a needle pricked her neck. Clara was still in darkness but the sound had gone. She felt nothing, not even her own body. She felt like a floating spirit trapped and inactive.

Suddenly, everything came back, sound, sight, smell. Every sense returned to her which caused an awful headache. Everything was a blear at first but as she felt her self fall forward, someone caught her and she was fine again. She looked up at the person holding her and smiled.

It was The Doctor.

They were stood in what appeared to be a Victorian sitting room which shared the same smell of mint and chemical that Clara had smelt near the lift. Mrs Gillyflower sat in an armchair, handcuffed to a radiator and in the corner stood a young woman with a scarred face and eyes the colour of mistletoe berries, dressed in a Victorian dress.

"I'm so glad to see you" The Doctor cried, grinning at her from ear to ear before pulling her into a tight hug.

"I saw you six hours ago" she laughed but stopped when he pulled away and looked at her with grave eyes.

"Clara, you have been missing almost a month."

"You WHAT?" she screeched, breathing quickly and heavily. "What happened? Is everything alright? DAD! Oh my stars, is he alright?"

"Your father is fine"The Doctor assured her. " Worried sick but fine. He's a nice bloke but he doesn't like the government."

"Oh thank goodness" she sighed with relief, attempting to run a hand through her hair but found it pinned in a strange Victorian style.

"Ah yes" The Doctor remembered. "I must tell you what happened. You see, I came into work and you weren't there so I thought you must be ill so I bought some Jammy Dodgers and went to your house. There, your father told me you hadn't come home and he had run the police. I...don't trust the police so I decided to find you myself. I pursued many lines of inquiry including questioning all who worked closely with you, talked to your friends, interrogated owners of rival companies and even tracked down some old boyfriends. You have dated some losers. Anyway, that is when Ada came to me" The Doctor ushered towards the woman who offered a smile in their direction. "She told me that her mother was taking people and you were one of them. She didn't know what was going on until she overheard her mother on the phone to someone. We confronted Mrs Gillyflower who admitted to it, telling us she was taking the 'perfect people' and keeping them safe by freezing their bodies in a venom like substance. That chemical smell is coming from you. She was planning to obliterate modern London and take it back to the Victorian era as shown through your period dress." Looking down, Clara saw she was wearing a Gothic Victorian dress with a corset underneath.

"I thought my clothes felt tighter" she managed to giggle before listening to the rest of The Doctor's story.

"It appears that Mrs Gillyflower is quite the steampunk. I have called you Dad and the police soI think we should begin getting the others back to normal, shall we."

Clara sat next to The Doctor on the back of one of the many ambulances that had arrived to care for those who, like her, had been drowned in the venom.

"Do you need to go talk to the police?" Clara asked her friend, pulling the shock blanket over herself more.

The Doctor nodded "Yes but not yet. I will stay with you."

"Well you may as well because my dad is here" she told him nodding towards the man running towards them.

He stood up and straightened his bow tie before kissing her forehead."Braveheart Clara" he whispered before leaving her at the mercy of her erratic father.

"I told you" he barked at her before giving her a hug. "I told you to be careful and look what happens. You are handing in your resignation tomorrow and we are moving somewhere safer."

"Dad no!" Clara protested but he didn't listen, dragging her to the car before driving away. Out of temptation or out of closure, Clara looked back on Torchwood which got smaller and smaller with each passing second. That was her chance at adventure and soon enough it was just another point on the skyline.

Clara lay awake, scowling at the roof. She had gone straight to her room when she got home, something she hadn't done since she was a teenager. However this time, she had good reason to be mad at her father. How could he be so selfish? She was living a brilliant dream, like something out of a TV show or a film, something unreal. Then with one move of parental power, he had taken it away from her.

She drew up plans as she lay there. She could get a flat closer to work and in the meantime she could stay in a hotel so her father would have no power over her. She could stay with a mate until he calmed down, she could defy him and go to work in secret. Or she could live with The Doctor for a bit. They could go out for dinner, watch the soaps on an evening, get breakfast before work at a little diner. That sounded good.

Her train of thought was broken when a stone hit her window. Getting up, Clara headed to the window and opened it, looking out to see The Doctor sat on a fold-up chair in her drive with a flask, about ten dozen cables and a plate of biscuits on a little table next to him. Upon seeing her he waved.

"Hello Clara" he called up with a grin.

"What are you doing?" Clara hissed at him. "Dad will kill you. He's already making me quit my job".

The Doctor shook his head with a proud smile. "I spoke to him and he agreed to let you carry on with your work on one condition."

"What condition?" She asked, smiling uncontrollably at the news of her fathers change of heart.

"That I protect you and I will" he replied happily. "So you go back to sleep because I want to do some tests in Rory's lab to see if you are one hundred percent alright. The family wedding was a bust by the way. The groom said another woman's name so it didn't end well. Anyway, goodnight."

"Night" she replied, closing her window before opening it again. "Are you guarding me?"

"Yes I suppose I am" he replied in amusement.

"Right, Why did Ada betray her mother?" Clara asked out of interest.

"The scarring on her face and her blindness was the result on her mother experimenting on her" he told her gravely."That was one of the things she found out of the phone. Somethings cannot be forgiven".

"But most things can" Clara added. "I forgive my father because unlike Mrs Gillyflower, he was only trying to protect me because he cared."

The Doctor smiled and held up the plate of biscuits. "Since you probably aren't tired since you have technically been asleep for a month which may affect your sleeping pattern for a while, sorry. Anyway, why don't you join me. The stars are beautiful tonight and I have ginger biscuits covered in chocolate with hot chocolate. That's almost as cool as bow ties!"

Clara laughed and closed her window before picking up her coat that lay on the floor. The adventure would continue tomorrow but for now she was going to relax with her impossible friend and look up at the stars.

**Dah Dah! I will update soon thanks for reading :)**


	10. Follower

**Sorry for the wait and the short chapter but I have been planning the next chapter. I promise the next chapter will make up for this :)**

The Doctor's promise to protect Clara was being taken more seriously than she thought. He was at her doorstep by eight and gave her a lift to school in his strange yellow car, saying good morning to her father beforehand which earned him some toast or a bagel if he was lucky. Upon arriving at work, he would escort Clara to her office and the pair would sit there until she got called up to one of the departments, The Doctor constantly in toe. After work, The Doctor would take her home and wit until her father returned home from work. Days off were worse with him arriving early in the morning and leaving late at night. Clara liked The Doctor but it was a little too much.

Once Clara found out The Doctor was in a meeting all afternoon, she was silently relieved. She decided to spend the afternoon with Amy who was celebrating the completion of her new report about the latest discoveries from the roman empire. Clara knew Amy was more interested in the actual events than the artifacts found so she was proud of her friends accomplishment. However, the main topic in conversation was not Roman pottery but the raggedy man with the bow tie.

"He won't give me a second to myself at work" Clara complained. "I like him but he is getting on my nerves now."

"He'll get over it" Amy assured her with a giggle. Unlike her friend, Amy found the whole thing very entertaining. "The Doctor is either really clingy or will keep people at arms length. He kept River at arms length for ages but he eventually settled into their friendship and then relationship. Me and him have always been close and it's the same with Rory. The Doctor likes having people around him. However, only certain people end up getting as close to him as we are. You know, if I were you I would be flattered."

"But you have Rory" Clara questioned, causing Amy to roll her eyes.

"I said if I were you. If he did it to me I'd get my water gun out."

Clara's eyes filled with hope but unfortunately her friend deduced what she was about to say and threw a pen at her.

"Just tell him to back off."

"I can't!" Clara cried. "I don't want to upset him with all his other problems and most of the time I like him being there, just not all the time."

Amy laughed and gave Clara a hug. "Just tell him that and he will understand. Trust me."

The Doctor reacted well to Clara's request and they compromised on him taking her to and from work and eating lunch with her. This surprised Clara as he had big news to share.

"I got it" he told her excitedly, almost jumping up in the air as he spoke.

"Got what?" Clara asked in confusion.

"The code to the vault" he said with the glee of a child. "Wanna go down and check it out".

"Yes, yes, yes" she replied instantly. "When shall we do it?"

"Tomorrow" he told her. "Come up here with me and we can use my service lift to get down there. Listen Clara, this could potentially be dangerous as things have been left down there for a reason. Anything could happen."

"That's what I'm counting on."

**Dun dun dun**


	11. The Vaults

**Sorry I haven't updated in so long but I am back with a vengeance! This is kinda short but I promise to update soon! Here's the next chapter, enjoy!**

****The vaults were underneath the tower in what was once a disused Victorian sewer system. The service lifts were the only way down there and as they were not the sci-fi lifts at the heart of the building, the journey down was a long one. This gave Clara the perfect opportunity to find out how The Doctor got the code in the first place.

"It was simple really" he began with a proud smile of achievement on his face. "I was looking for old software I could adapt to make my face-recognition scanner work. Then there it was. Imagine what parts I could find down here. I could build everything I ever dreamed of."

"So you changed the name of The Face Matcher?" Clara asked in amusement.

The Doctor nodded "it sounds cooler".

Clara was about to comment but the lift stopped with a thud. It had been a while since Clara had used a normal lift and she left rather woozy once the metal box stopped moving. The Doctor seemed unfazed by the whole thing as per usual and sped out of the lift as soon as the doors opened.

The small cubic space they entered smelt damp and smoky. The walls were concrete and were stained with something Clara didn't know and didn't want to know. Opposite the lifts doors was a similar one with a screen next to it. The Doctor dashed towards it and typed in the word 'Abigail'.

"Whose Abigail?" Clara asked and The Doctor shrugged in reply.

"That on my mystery list" he smiled with a spark of madness in his eyes as he pressed enter. The metal doors slowly opened to reveal a tunnel lined with the weird and the wonderful like the corridor of a museum.

"This is amazing" The Doctor gasped with a grin. He instantly began looking at everything from bottled liquids to skeletal models of extinct animals. Clara followed him for what seemed like hours and even though The Doctor found it all so interesting, she found it rather boring.

"Can we go back now" she asked, causing him to stop walking and glare at her.

"This is the adverts Clara" he replied. "Do you leave the cinema because the adverts are boring?"

"No"

"Then come on!"

She followed him for what seemed like forever. They passed millions upon thousands of spare parts, filing cabinets and random bits of junk until the trail ended at another door with another screen requesting a password.

"Got that one two?"Clara asked and The Doctor nodded and typed in the word 'Pettigrew'.

"I believe this also has something to do with that is for another day". The Doctor clapped his hands together and waited for the doors to open. It took a while as the door was much older than the last and was rather stiff, as though it hadn't been opened for a very long time.

As soon as the door opened, we stepped through it and it slammed shut behind us.

"Motion sensors?" Clara asked but The Doctor shook his head.

"It's probably a way to shut out those who go meddling. However I am a professional meddler and you are a natural".

Clara didn't know whether to take it as a compliment or an insult so said nothing. But then she saw what lay ahead of her and became well and truly speechless...

**I will upload again in the next few days hopefully :) **


	12. What Came Next

**Next chapter time!**

****Clara could now see why this door stood between the piles of junk and what stood in front of them. This was why people weren't allowed down there, this was why there were so many secrets, this was-

"Brilliant" The Doctor cheered with glee. He had acted the same before but Clara had to agree with him this time as this was not a storage for junk, this was a storage for genius! Various machines of all different shapes and sizes surrounded them in one huge man-made cave hidden under the centre of London.

They began to walk forward in complete silence, taking everything in. There were little flying saucers mounted onto thick sheets of steel, thick glass cases holding various energies and chemical reactions that The Doctor branded 'impossible', stuffed creatures held in metal cages with labels that read 'risk of infection' next to a skull and cross bones. These were the secrets of the universe and millions had walked over it not knowing what lay beneath their feet.

"Doctor, is this safe?" Clara asked after a while and he shrugged.

"I thought you liked danger?" he teased with a childish grin, skipping along ahead of her.

"Yes but there's danger like risking-breaking-a-bone danger and then there's danger like risking-your-life danger" she pointed out, causing him to laugh.

"Oh come on Clara, do you really think I would put you in that much danger. Anyway even if you did get hurt we could just get in the lift and go to Rory. He'd be able to fix you up in time for tea."

"Doctor, you..." she began but something court her eye. It was a white box, big enough to stand in, with a counter that was stuck at one underneath a small circular window that was fogged over, causing it's contents to be hidden. Clara walked towards it slowly and as soon as she got to the widow, she moved her hand across the small window. It was mostly dust but some of hit was condensation and she found the glass to be well over ice cold. Eventually she was able to see and when she did she let out an ear-piercing scream and jumped away from it.

"Clara, whats wrong?" The Doctor asked, running towards her.

"The-the-there's a woman in there" she stammered in a panic and The Doctor went over to investigate the box. When he saw what was inside, he frowned.

From his pocket he pulled out a device he had seen The Doctor working on many times before.

"You finished the Sonic Screwdriver?" she questioned and he nodded.

"Yes, while you were missing. I thought it may help."

He pointed the device at the lock on the boxes door and a strange buzzing sound came from it. The door clicked and The Doctor pulled it open. White smoke filled the air and as soon as it cleared, the woman was awake and being helped out of her container by The Doctor.

"What year is it?" she asked but The Doctor ignored her and shook her hand.

"Hello, I'm The Doctor and this is Clara. We're just passing by. What would your name be?"

"Abigail" she replied with sweet smile. "Now can you tell me what year it is."

"Oh Abigail, you're that password you know"he chattered on yet again. "I've never been a password except for..."

Clara cut him off by stamping on his foot and stepped forward to greet Abigail properly. "Sorry abut that. It's the year 2013 and we work for Torchwood. Do you know what that it?"

"Yes I do" Abigail replied, looking rather taken aback by the year.

"Really?" The Doctor butted in and stepped in front of Clara and causing her to fall backwards.

She landed on something and it began to beep. Suddenly there was a noise that sounded like some kind of rhythmic machine. The expression on The Doctor's face dropped from a giddy smile to a look of terror which made Clara's stomach churn.

"Doctor, what is it?" She asked, pulling herself to her feet.

"We need to get out of here now."

**I know this was rubbish but considering there is an argument going on between my friends on Facebook as we speak, I think I did okay. I'll hopefully update sometime this week, definitely before Friday :)**


	13. Wasting Time

**Sorry this is pushing my self-set deadline :/ I have learnt this week that 6th form is horrible and stressful so hopefully Friends will chill me out. Enjoy!**

****Upon hearing those words leave his lips, Clara felt sick. The Doctor was never one to cower in the face of danger yet here he was, practically shaking with eyes like a terrified child. Her hero had last his nerve and now it was up to her to take the lead.

Quickly, Clara took Abigail's hands and grabbed the sleeve of The Doctor's coat.

"Alright, we need to go back the way we came, yeah?"She asked her terrified friend who nodded.

"Yes, use the same password we used to open it the first time and get straight through" he managed to reply, not taking his eyes away from the direction of the noise. "Then you need to head straight to the lift and get the hell out of here. When we do, take Abigail to Rory to get her checked over. Tell him what has happened and he will know what to do".

"Can't you?" Clara asked before catching on to what he meant. "No you are not staying down here!"

"Clara I have to" he insisted. "I have a responsibility but you don't. You're technically a civilian and someone needs to get Abigail out of here."

"Then let it be me" she argued desperately. "They need you up there and you would be able to get Abigail out of here faster than me. You run a lot faster even though you're a bit clumsy and you are good at improvising. No one needs me and no one will notice I'm gone".

"I would" he barely whispered. "So would Amy and Rory but most of all, you have you're father, a family. I don't. I've lost it all. No one would miss me a sixth as much as people would miss you".

He was right and she hated it. She couldn't stay down here to battle whatever was coming closer and closer with every metal footstep and ruin her fathers life yet again. However that didn't mean The Doctor was staying either.

"We both get out of here" she suggested with a hopeful smile. "We get out of here and think about what to do when we aren't in a vault underground with something coming for us."

The Doctors face broke out into a smile. "I like your thinking. If we could just get them to stay down here, we could get back and I could try and think of a plan. Yes, that sounds like a good plan. Right now, we need to get Abigail out of here."

They both suddenly became aware Abigail had been stood there silently the whole time. She looked confused and almost as terrified as The Doctor was. Clara figured that whatever it was, it had been down here as long as she had. Even though she was clearly the only one who didn't know what was coming for them, Clara thought of herself as having the upper hand. She knew it was dangerous but was not blinded by the fear and maybe, just maybe, that would make the plan work. She smiled confidently, now high on the adrenaline, and clapped her hands together.

"Okay then, lets run".

The way they had come from seemed like a maze compared to when their little stroll through the strange objects and extraudinary odities. The Doctor ran ahead, pulling Abigail along while Clara was close behind. As they got closer to the door, The Doctor took a swift short cut, trailing the two girls the same way too. Clara was close behind them but then something caught her eye. Even in an ark of impossible things, the smallest thing, the most normal thing, was the most important.

A blue diary in the style of a police box.

She picked it up and ran her and along the cover. This was it. The thing that may have cost River Song her life. She looked ahead to see if The Doctor was watching but he was still running along, his back turned to her. Swiftly she carefully put the diary in the red satchel she always carried. There was no way she could leave it down there without knowing what lay inside.

Once she finished sealing her bag back up, she realized the noise had stopped. She looked up slowly and froze to the spot. The Doctor and Abigail were right to be afraid. It was a man of metal with an emotionless face that made her blood run cold. In a robotic voice, the metal man spoke.

"You will be upgraded".

There was only one thing to do and one thing only.

"DOCTOR!" she cried before running away as fast as her legs could carry her, the metal man in hot pursuit.

**There you go guys :) I know it's bad but soon things will start making sense I promise :)**


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